------------------------------------------------------- Amber 20 PMEMD 2020 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 18 | Executable base on git commit: 5582ead046263fa35196b75ad7a34d5162126b1e | Compiled date/time: Fri Sep 17 14:20:38 2021 | Compiled on: rioja-rutgers-edu | Compiled by: taisung | Run on 10/04/2022 at 14:27:33 | Executable path: pmemd | Working directory: /Users/msuruzhon/Projects/bss_orion/temp/31460/wt~T113Y_FID_A_pdb/bound/Pre_Minimisation/lambda_0.0000/test/reproduce | Hostname: Unknown | WARNING: Stack usage limited by a hard resource limit of 67104768 bytes! | If segment violations occur, get your sysadmin to increase the limit. [-O]verwriting output File Assignments: | MDIN: amber.mdin | MDOUT: amber.out | INPCRD: amber.rst7 | PARM: amber.parm7 | RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo | MDFRC: mdfrc Here is the input file: FreeEnergyMinimisation &cntrl ntpr=200, ntxo=2, irest=0, ntx=1, imin=1, ntmin=2, maxcyc=10000, ncyc=1000, cut=8.0, iwrap=0, icfe=1, ifsc=1, ntf=1, ntb=1, mbar_states=11, mbar_lambda=0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, clambda=0.0, timask1="@17-30", timask2="@31-51", scmask1="@22-23,27-30", scmask2="@39-51", noshakemask="", / Note: ig = -1. Setting random seed to 193559 based on wallclock time in microseconds. | irandom = 1, using AMBER's internal random number generator (default). | Conditional Compilation Defines Used: | PUBFFT | BINTRAJ | EMIL | Largest sphere to fit in unit cell has radius = 20.000 | New format PARM file being parsed. | Version = 1.000 Date = 10/04/22 Time = 14:16:07 | Note: 1-4 EEL scale factors are being read from the topology file. | Note: 1-4 VDW scale factors are being read from the topology file. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting new box info from bottom of inpcrd NATOM = 59 NTYPES = 11 NBONH = 28 MBONA = 33 NTHETH = 65 MTHETA = 46 NPHIH = 140 MPHIA = 110 NHPARM = 0 NPARM = 0 NNB = 350 NRES = 3 NBONA = 33 NTHETA = 46 NPHIA = 110 NUMBND = 16 NUMANG = 20 NPTRA = 59 NATYP = 11 NPHB = 0 IFBOX = 1 NMXRS = 35 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 8 8 8 | Direct force subcell size = 5.0000 5.0000 5.0000 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- BioSimSpace System General flags: imin = 1, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 2, ntpr = 200, ntrx = 1, ntwr = 1 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 10000, ncyc = 1000, ntmin = 2 dx0 = 0.01000, drms = 0.00010 Free energy options: icfe = 1, ifsc = 1, klambda = 1 clambda = 0.0000, scalpha = 0.5000, scbeta = 12.0000 sceeorder = 2 dynlmb = 0.0000 logdvdl = 0 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 1 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 0 Box X = 40.000 Box Y = 40.000 Box Z = 40.000 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 40 NFFT2 = 40 NFFT3 = 40 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 TI Mask 1 @17-30; matches 14 atoms TI Mask 2 @31-51; matches 21 atoms TI region 1: 38 atoms TI region 2: 45 atoms SC Mask 1 @22-23,27-30; matches 6 atoms SC Mask 2 @39-51; matches 13 atoms -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- BioSimSpace System begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 Number of shake restraints removed in TI region 1 : 0 Number of shake restraints removed in TI region 2 : 0 Sum of charges for TI region 1 = -0.00000001 Forcing neutrality... Sum of charges for TI region 2 = -0.00000001 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 125904 | Integers 8997 | Nonbonded Pairs Initial Allocation: 9854 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION using 5000.0 points per unit in tabled values TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960 --------------------------------------------------- |--------------------------------------------------- | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.47 | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.89 |--------------------------------------------------- | TI region 1 NSTEP ENERGY RMS GMAX NAME NUMBER 1 NaN NaN 4.8378E+05 O 20 BOND = 25.5950 ANGLE = 10.3556 DIHED = 17.7623 VDWAALS = -0.1730 EEL = NaN HBOND = 0.0000 1-4 VDW = 74267.8054 1-4 EEL = -12.9967 RESTRAINT = 0.0000 DV/DL = NaN